Algoritmi di ottimizzazione per il bus touring problem.

Nel campo della Ricerca Operativa e dei problemi di ottimizzazione viene presentato un problema, denominato Bus Touring Problem (BTP), che modella una problematica riguardante il carico e l’instradamento di veicoli nella presenza di di vincoli temporali e topologici sui percorsi. Nel BTP, ci si pone il problema di stabilire una serie di rotte per la visita di punti di interesse dislocati geograficamente da parte di un insieme di comitive turistiche, ciascuna delle quali stabilisce preferenze riguardo le visite. Per gli spostamenti sono disponibili un numero limitato di mezzi di trasporto, in generale eterogenei, e di capacitá limitata. Le visite devono essere effettuate rispettando finestre temporali che indicano i periodi di apertura dei punti di interesse; per questi, inoltre, é specificato un numero massimo di visite ammesse. L’obiettivo é di organizzare il carico dei mezzi di trasporto e le rotte intraprese in modo da massimizzare la soddisfazione complessiva dei gruppi di turisti nel rispetto dei vincoli imposti. Viene presentato un algoritmo euristico basato su Tabu Search appositamente ideato e progettato per la risoluzione del BTP. Vengono presentati gli esperimenti effettuati riguardo la messa appunto dei parametri dell'algoritmo su un insieme di problemi di benchmark. Vengono presentati risultati estesi riguardo le soluzioni dei problemi. Infine, vengono presentate considerazioni ed indicazioni di sviluppo futuro in materia.

Hierarchical Approach for Survivable Network Design

A central design challenge facing network planners is how to select a cost-effective network configuration that can provide uninterrupted service despite edge failures. In this paper, we study the Survivable Network Design (SND) problem, a core model underlying the design of such resilient networks that incorporates complex cost and connectivity trade-offs. Given an undirected graph with specified edge costs and (integer) connectivity requirements between pairs of nodes, the SND problem seeks the minimum cost set of edges that interconnects each node pair with at least as many edge-disjoint paths as the connectivity requirement of the nodes. We develop a hierarchical approach for solving the problem that integrates ideas from decomposition, tabu search, randomization, and optimization. The approach decomposes the SND problem into two subproblems, Backbone design and Access design, and uses an iterative multi-stage method for solving the SND problem in a hierarchical fashion. Since both subproblems are NP-hard, we develop effective optimization-based tabu search strategies that balance intensification and diversification to identify near-optimal solutions. To initiate this method, we develop two heuristic procedures that can yield good starting points. We test the combined approach on large-scale SND instances, and empirically assess the quality of the solutions vis-à-vis optimal values or lower bounds. On average, our hierarchical solution approach generates solutions within 2.7% of optimality even for very large problems (that cannot be solved using exact methods), and our results demonstrate that the performance of the method is robust for a variety of problems with different size and connectivity characteristics.

The information bottleneck method for genome-wide association studies

In population studies, most current methods focus on identifying one outcome-related SNP at a time by testing for differences of genotype frequencies between disease and healthy groups or among different population groups. However, testing a great number of SNPs simultaneously has a problem of multiple testing and will give false-positive results. Although, this problem can be effectively dealt with through several approaches such as Bonferroni correction, permutation testing and false discovery rates, patterns of the joint effects by several genes, each with weak effect, might not be able to be determined. With the availability of high-throughput genotyping technology, searching for multiple scattered SNPs over the whole genome and modeling their joint effect on the target variable has become possible. Exhaustive search of all SNP subsets is computationally infeasible for millions of SNPs in a genome-wide study. Several effective feature selection methods combined with classification functions have been proposed to search for an optimal SNP subset among big data sets where the number of feature SNPs far exceeds the number of observations. ^ In this study, we take two steps to achieve the goal. First we selected 1000 SNPs through an effective filter method and then we performed a feature selection wrapped around a classifier to identify an optimal SNP subset for predicting disease. And also we developed a novel classification method-sequential information bottleneck method wrapped inside different search algorithms to identify an optimal subset of SNPs for classifying the outcome variable. This new method was compared with the classical linear discriminant analysis in terms of classification performance. Finally, we performed chi-square test to look at the relationship between each SNP and disease from another point of view. ^ In general, our results show that filtering features using harmononic mean of sensitivity and specificity(HMSS) through linear discriminant analysis (LDA) is better than using LDA training accuracy or mutual information in our study. Our results also demonstrate that exhaustive search of a small subset with one SNP, two SNPs or 3 SNP subset based on best 100 composite 2-SNPs can find an optimal subset and further inclusion of more SNPs through heuristic algorithm doesn't always increase the performance of SNP subsets. Although sequential forward floating selection can be applied to prevent from the nesting effect of forward selection, it does not always out-perform the latter due to overfitting from observing more complex subset states. ^ Our results also indicate that HMSS as a criterion to evaluate the classification ability of a function can be used in imbalanced data without modifying the original dataset as against classification accuracy. Our four studies suggest that Sequential Information Bottleneck(sIB), a new unsupervised technique, can be adopted to predict the outcome and its ability to detect the target status is superior to the traditional LDA in the study. ^ From our results we can see that the best test probability-HMSS for predicting CVD, stroke,CAD and psoriasis through sIB is 0.59406, 0.641815, 0.645315 and 0.678658, respectively. In terms of group prediction accuracy, the highest test accuracy of sIB for diagnosing a normal status among controls can reach 0.708999, 0.863216, 0.639918 and 0.850275 respectively in the four studies if the test accuracy among cases is required to be not less than 0.4. On the other hand, the highest test accuracy of sIB for diagnosing a disease among cases can reach 0.748644, 0.789916, 0.705701 and 0.749436 respectively in the four studies if the test accuracy among controls is required to be at least 0.4. ^ A further genome-wide association study through Chi square test shows that there are no significant SNPs detected at the cut-off level 9.09451E-08 in the Framingham heart study of CVD. Study results in WTCCC can only detect two significant SNPs that are associated with CAD. In the genome-wide study of psoriasis most of top 20 SNP markers with impressive classification accuracy are also significantly associated with the disease through chi-square test at the cut-off value 1.11E-07. ^ Although our classification methods can achieve high accuracy in the study, complete descriptions of those classification results(95% confidence interval or statistical test of differences) require more cost-effective methods or efficient computing system, both of which can't be accomplished currently in our genome-wide study. We should also note that the purpose of this study is to identify subsets of SNPs with high prediction ability and those SNPs with good discriminant power are not necessary to be causal markers for the disease.^

Spatial sampling methods for improved communication for wireless relay robots

Having reliable wireless communication in a network of mobile robots is an ongoing challenge, especially when the mobile robots are given tasks in hostile or harmful environments such as radiation environments in scientific facilities, tunnels with large metallic components and complicated geometries as found at CERN. In this paper, we propose a decentralised method for improving the wireless network throughput by optimizing the wireless relay robot position to receive the best wireless signal strength using implicit spatial diversity concepts and gradient-search algorithms. We experimentally demonstrate the effectiveness of the proposed solutions with a KUKA Youbot omni-directional mobile robot. The performance of the algorithms is compared under various scenarios in an underground scientific facility at CERN.

WSM : metodología de web scraping para Android y ejemplificación mediante la aplicación UPMDroid

En la realización de este proyecto se ha tratado principalmente la temática del web scraping sobre documentos HTML en Android. Como resultado del mismo, se ha propuesto una metodología para poder realizar web scraping en aplicaciones implementadas para este sistema operativo y se desarrollará una aplicación basada en esta metodología que resulte útil a los alumnos de la escuela. Web scraping se puede definir como una técnica basada en una serie de algoritmos de búsqueda de contenido con el fin de obtener una determinada información de páginas web, descartando aquella que no sea relevante. Como parte central, se ha dedicado bastante tiempo al estudio de los navegadores y servidores Web, y del lenguaje HTML presente en casi todas las páginas web en la actualidad así como de los mecanismos utilizados para la comunicación entre cliente y servidor ya que son los pilares en los que se basa esta técnica. Se ha realizado un estudio de las técnicas y herramientas necesarias, aportándose todos los conceptos teóricos necesarios, así como la proposición de una posible metodología para su implementación. Finalmente se ha codificado la aplicación UPMdroid, desarrollada con el fin de ejemplificar la implementación de la metodología propuesta anteriormente y a la vez desarrollar una aplicación cuya finalidad es brindar al estudiante de la ETSIST un soporte móvil en Android que le facilite el acceso y la visualización de aquellos datos más importantes del curso académico como son: el horario de clases y las calificaciones de las asignaturas en las que se matricule. Esta aplicación, además de implementar la metodología propuesta, es una herramienta muy interesante para el alumno, ya que le permite utilizar de una forma sencilla e intuitiva gran número de funcionalidades de la escuela solucionando así los problemas de visualización de contenido web en los dispositivos. ABSTRACT. The main topic of this project is about the web scraping over HTML documents on Android OS. As a result thereof, it is proposed a methodology to perform web scraping in deployed applications for this operating system and based on this methodology that is useful to the ETSIST school students. Web scraping can be defined as a technique based on a number of content search algorithms in order to obtain certain information from web pages, discarding those that are not relevant. As a main part, has spent considerable time studying browsers and Web servers, and the HTML language that is present today in almost all websites as well as the mechanisms used for communication between client and server because they are the pillars which this technique is based. We performed a study of the techniques and tools needed, providing all the necessary theoretical concepts, as well as the proposal of a possible methodology for implementation. Finally it has codified UPMdroid application, developed in order to illustrate the implementation of the previously proposed methodology and also to give the student a mobile ETSIST Android support to facilitate access and display those most important data of the current academic year such as: class schedules and scores for the subjects in which you are enrolled. This application, in addition to implement the proposed methodology is also a very interesting tool for the student, as it allows a simple and intuitive way of use these school functionalities thus fixing the viewing web content on devices.

The optimization principle in phylogenetic analysis tends to give incorrect topologies when the number of nucleotides or amino acids used is small

In the maximum parsimony (MP) and minimum evolution (ME) methods of phylogenetic inference, evolutionary trees are constructed by searching for the topology that shows the minimum number of mutational changes required (M) and the smallest sum of branch lengths (S), respectively, whereas in the maximum likelihood (ML) method the topology showing the highest maximum likelihood (A) of observing a given data set is chosen. However, the theoretical basis of the optimization principle remains unclear. We therefore examined the relationships of M, S, and A for the MP, ME, and ML trees with those for the true tree by using computer simulation. The results show that M and S are generally greater for the true tree than for the MP and ME trees when the number of nucleotides examined (n) is relatively small, whereas A is generally lower for the true tree than for the ML tree. This finding indicates that the optimization principle tends to give incorrect topologies when n is small. To deal with this disturbing property of the optimization principle, we suggest that more attention should be given to testing the statistical reliability of an estimated tree rather than to finding the optimal tree with excessive efforts. When a reliability test is conducted, simplified MP, ME, and ML algorithms such as the neighbor-joining method generally give conclusions about phylogenetic inference very similar to those obtained by the more extensive tree search algorithms.

The emotif database

The emotif database is a collection of more than 170 000 highly specific and sensitive protein sequence motifs representing conserved biochemical properties and biological functions. These protein motifs are derived from 7697 sequence alignments in the BLOCKS+ database (released on June 23, 2000) and all 8244 protein sequence alignments in the PRINTS database (version 27.0) using the emotif-maker algorithm developed by Nevill-Manning et al. (Nevill-Manning,C.G., Wu,T.D. and Brutlag,D.L. (1998) Proc. Natl Acad. Sci. USA, 95, 5865–5871; Nevill-Manning,C.G., Sethi,K.S., Wu,T.D. and Brutlag,D.L. (1997) ISMB-97, 5, 202–209). Since the amino acids and the groups of amino acids in these sequence motifs represent critical positions conserved in evolution, search algorithms employing the emotif patterns can identify and classify more widely divergent sequences than methods based on global sequence similarity. The emotif protein pattern database is available at http://motif.stanford.edu/emotif/.

State of the art in continuous speech recognition.

In the past decade, tremendous advances in the state of the art of automatic speech recognition by machine have taken place. A reduction in the word error rate by more than a factor of 5 and an increase in recognition speeds by several orders of magnitude (brought about by a combination of faster recognition search algorithms and more powerful computers), have combined to make high-accuracy, speaker-independent, continuous speech recognition for large vocabularies possible in real time, on off-the-shelf workstations, without the aid of special hardware. These advances promise to make speech recognition technology readily available to the general public. This paper focuses on the speech recognition advances made through better speech modeling techniques, chiefly through more accurate mathematical modeling of speech sounds.

Exploring automatic feature selection for transition-based dependency parsing

En este artículo se investigan técnicas automáticas para encontrar un modelo óptimo de características en el caso de un analizador de dependencias basado en transiciones. Mostramos un estudio comparativo entre algoritmos de búsqueda, sistemas de validación y reglas de decisión demostrando al mismo tiempo que usando nuestros métodos es posible conseguir modelos complejos que proporcionan mejores resultados que los modelos que siguen configuraciones por defecto.

Teleonomic entropy: measuring the phase-space of end-directed systems

We introduce a novel way of measuring the entropy of a set of values undergoing changes. Such a measure becomes useful when analyzing the temporal development of an algorithm designed to numerically update a collection of values such as artificial neural network weights undergoing adjustments during learning. We measure the entropy as a function of the phase-space of the values, i.e. their magnitude and velocity of change, using a method based on the abstract measure of entropy introduced by the philosopher Rudolf Carnap. By constructing a time-dynamic two-dimensional Voronoi diagram using Voronoi cell generators with coordinates of value- and value-velocity (change of magnitude), the entropy becomes a function of the cell areas. We term this measure teleonomic entropy since it can be used to describe changes in any end-directed (teleonomic) system. The usefulness of the method is illustrated when comparing the different approaches of two search algorithms, a learning artificial neural network and a population of discovering agents. (C) 2004 Elsevier Inc. All rights reserved.

Hyperspace geography: Visualizing fitness landscapes beyond 4D

Human perception is finely tuned to extract structure about the 4D world of time and space as well as properties such as color and texture. Developing intuitions about spatial structure beyond 4D requires exploiting other perceptual and cognitive abilities. One of the most natural ways to explore complex spaces is for a user to actively navigate through them, using local explorations and global summaries to develop intuitions about structure, and then testing the developing ideas by further exploration. This article provides a brief overview of a technique for visualizing surfaces defined over moderate-dimensional binary spaces, by recursively unfolding them onto a 2D hypergraph. We briefly summarize the uses of a freely available Web-based visualization tool, Hyperspace Graph Paper (HSGP), for exploring fitness landscapes and search algorithms in evolutionary computation. HSGP provides a way for a user to actively explore a landscape, from simple tasks such as mapping the neighborhood structure of different points, to seeing global properties such as the size and distribution of basins of attraction or how different search algorithms interact with landscape structure. It has been most useful for exploring recursive and repetitive landscapes, and its strength is that it allows intuitions to be developed through active navigation by the user, and exploits the visual system's ability to detect pattern and texture. The technique is most effective when applied to continuous functions over Boolean variables using 4 to 16 dimensions.

Palette-colouring: a belief propagation approach

We consider a variation of the prototype combinatorial optimization problem known as graph colouring. Our optimization goal is to colour the vertices of a graph with a fixed number of colours, in a way to maximize the number of different colours present in the set of nearest neighbours of each given vertex. This problem, which we pictorially call palette-colouring, has been recently addressed as a basic example of a problem arising in the context of distributed data storage. Even though it has not been proved to be NP-complete, random search algorithms find the problem hard to solve. Heuristics based on a naive belief propagation algorithm are observed to work quite well in certain conditions. In this paper, we build upon the mentioned result, working out the correct belief propagation algorithm, which needs to take into account the many-body nature of the constraints present in this problem. This method improves the naive belief propagation approach at the cost of increased computational effort. We also investigate the emergence of a satisfiable-to-unsatisfiable 'phase transition' as a function of the vertex mean degree, for different ensembles of sparse random graphs in the large size ('thermodynamic') limit.

The System of Quality Prediction on the Basis of a Fuzzy Data and Psychography of the Experts

The system of development unstable processes prediction is given. It is based on a decision-tree method. The processing technique of the expert information is offered. It is indispensable for constructing and processing by a decision-tree method. In particular data is set in the fuzzy form. The original search algorithms of optimal paths of development of the forecast process are described. This one is oriented to processing of trees of large dimension with vector estimations of arcs.

Differential Balanced Trees and (0,1) Matrices

* The research was supported by INTAS 00-397 and 00-626 Projects.

Использование Алгоритма Ускоренного Вероятностного Моделирования в Схеме Табу-Поиска

Рассматривается метаэвристический метод комбинаторной оптимизации, основанный на использовании алгоритмов табу-поиска и ускоренного вероятностного моделирования. Излагается общая вычислительная схема предложенного метода, названного алгоритмом GS-tabu. Приведены результаты серии вычислительных экспериментов по решению известных задач коммивояжера и квадратичных задач о назначении.